## ----setup, include=FALSE------------------------------------------------
knitr::opts_chunk$set(echo = TRUE, warnings = FALSE, message = FALSE,fig.height = 3, fig.width = 5)
## ------------------------------------------------------------------------
MASS::data("cats")
## ------------------------------------------------------------------------
dim(cats)
summary(cats)
## ------------------------------------------------------------------------
library(doBy)
#get the mean and SD
cat.df1 <- summaryBy(Bwt ~ Sex, data = cats, FUN = c(mean,sd))
#get the sample size using length()
cat.df2 <- summaryBy(Bwt ~ Sex, data = cats, FUN = c(length))
#make a combined dataframe
cat.df3 <- merge(cat.df1,cat.df2)
#calculate the standard error SE by hand
cat.df3$SE <- cat.df3$Bwt.sd/sqrt(cat.df3$Bwt.length)
## ------------------------------------------------------------------------
cat.df3
## ------------------------------------------------------------------------
par(mfrow = c(1,1),mar = c(3,3.5,1,1))
boxplot(Bwt ~ Sex, data = cats)
## ------------------------------------------------------------------------
library(Hmisc)
par(mfrow = c(1,2),mar = c(3,3.5,1,1))
y.lim <- c(2.295,3)
errbar(1:2,
y = cat.df3$Bwt.mean,
yplus =cat.df3$Bwt.mean + cat.df3$SE,
yminus = cat.df3$Bwt.mean-cat.df3$SE,
xlab = "",
ylab = "",
xlim=c(0.5,2.5),
ylim = y.lim,
xaxt="n",cex =1)
axis(side=1,at=1:2,labels=cat.df3$Sex)
mtext("Sex", side = 1, line = 2, cex = 2)
mtext("Mass (g)", side = 2, line = 2.1, cex = 1.3)
errbar(1:2,
y = cat.df3$Bwt.mean,
yplus =cat.df3$Bwt.mean + 1.96*cat.df3$SE,
yminus = cat.df3$Bwt.mean-1.96*cat.df3$SE,
xlab = "",
ylab = "",
xlim=c(0.5,2.5),
ylim = y.lim,
xaxt="n",cex =1)
axis(side=1,at=1:2,labels=cat.df3$Sex)
mtext("Sex", side = 1, line = 2, cex = 2)
mtext("Mass (g)", side = 2, line = 2.1, cex = 1.3)
## ------------------------------------------------------------------------
cat.df3.mod <- cat.df3
cat.df3.mod$Bwt.mean[1] <- cat.df3$Bwt.mean[2]-cat.df3$Bwt.mean[2]*0.0425
## ------------------------------------------------------------------------
y.lim <- c(2.6975,3)
par(mar = c(3,3.5,1,1))
errbar(1:2,
y = cat.df3.mod$Bwt.mean,
yplus =cat.df3.mod$Bwt.mean + cat.df3.mod$SE,
yminus = cat.df3.mod$Bwt.mean-cat.df3.mod$SE,
xlab = "",
ylab = "",
xlim=c(0.5,2.5),
ylim = y.lim,
xaxt="n",cex =1)
axis(side=1,at=1:2,labels=cat.df3.mod$Sex)
mtext("Sex", side = 1, line = 2, cex = 2)
mtext("Mass (g)", side = 2, line = 2.1, cex = 1.3)
errbar(1:2,
y = cat.df3.mod$Bwt.mean,
yplus =cat.df3.mod$Bwt.mean + 1.96*cat.df3.mod$SE,
yminus = cat.df3.mod$Bwt.mean-1.96*cat.df3.mod$SE,
xlab = "",
ylab = "",
xlim=c(0.5,2.5),
ylim = y.lim,
xaxt="n",cex =1)
axis(side=1,at=1:2,labels=cat.df3.mod$Sex)
mtext("Sex", side = 1, line = 2, cex = 2)
mtext("Mass (g)", side = 2, line = 2.1, cex = 1.3)
## ------------------------------------------------------------------------
t.test(Bwt ~ Sex, data = cats)
## ------------------------------------------------------------------------
summary(lm(Bwt ~ -1+Sex, data = cats))
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